biosigner (version 1.0.4)

plot.biosign: Plot method for 'biosign' signature objects

Description

Displays classifier tiers or individual boxplots from selected features

Usage

## S3 method for class 'biosign':
plot(x,
y,
tierMaxC = "S",
typeC = c("tier", "boxplot")[1],
file.pdfC = NULL,
.sinkC = NULL,
...)

Arguments

x

An S4 object of class biosign, created by the biosign function.

y

Currently not used.

tierMaxC

Character: Maximum level of tiers to display: Either 'S' and 'A', (for boxplot), or also 'B', 'C', 'D', and 'E' (for tiers) by decreasing number of selections

typeC

Character: Plot type; either 'tier' [default] displaying the comparison of signatures up to the selected 'tierMaxC' or 'boxplot' showing the individual boxplots of the features selected by all the classifiers

file.pdfC

Character: Figure filename ending with '.pdf'; default is NULL (no saving; displaying instead)

.sinkC

Character: Name of the file for R output diversion [default = NULL: no diversion]; Diversion of messages is required for the integration into Galaxy

...

Currently not used.

Value

• A plot is created on the current graphics device.

Examples

## loading the diaplasma dataset

data(diaplasma)
attach(diaplasma)

## restricting to a smaller dataset for this example

featureSelVl <- variableMetadata[, "mzmed"] >= 490 & variableMetadata[, "mzmed"] < 500
dataMatrix <- dataMatrix[, featureSelVl]
variableMetadata <- variableMetadata[featureSelVl, ]

## signature selection for all 3 classifiers
## a bootI = 5 number of bootstraps is used for this example
## we recommend to keep the default bootI = 50 value for your analyzes

set.seed(123)
diaSign <- biosign(dataMatrix, sampleMetadata[, "type"], bootI = 5)

## individual boxplot of the selected signatures

plot(diaSign, typeC = "boxplot")

detach(diaplasma)